Issues

• Publish Sid SV audit checkpoints atomically outside reconstruction deadlines

  openvax/isovar#435 · Filter by author iskandr opened on Oct 2, 2026

• Split oversized Sid SV acquisition batches without losing other targets

  openvax/isovar#434 · Filter by author iskandr opened on Oct 2, 2026

• Adopt the mhctools documentation style

  openvax/isovar#432 · Filter by author iskandr opened on Oct 2, 2026

• in_cis: estimate read error rates per locus and direction (ONT, homopolymer indels, RNA editing)

  openvax/isovar#411 · Filter by author iskandr opened on Sep 28, 2026

• Infer adapter profiles from bounded read samples when exact sequences are not supplied

  openvax/isovar#309 · Filter by author iskandr opened on Sep 18, 2026

• Reconcile nominated large indel and SV interpretations using RNA assemblies and read-path evidence

  openvax/isovar#306 · Filter by author iskandr opened on Sep 18, 2026
  1

• Reconstruct alternative SV RNA paths and reconcile them with transcript/protein hypotheses

  openvax/isovar#305 · Filter by author iskandr opened on Sep 18, 2026
  1

• Recognize adapter-derived sequence when reusing soft clips for assembly or SV evidence

  openvax/isovar#302 · Filter by author iskandr opened on Sep 18, 2026
  2

• Move recorded performance evidence and its audit tests out of the test suite

  openvax/isovar#246 · Filter by author iskandr opened on Sep 14, 2026

• Share coordinates while building each LocusRead instead of rebuilding its list afterwards

  openvax/isovar#241 · Filter by author iskandr opened on Sep 14, 2026

• Collection benchmark fingerprint ignores sequence container types, and its Variant binds an unpinned genome

  openvax/isovar#237 · Filter by author iskandr opened on Sep 11, 2026
  2

• Share run-collection and pair-comparison logic between performance_report and collection_report

  openvax/isovar#235 · Filter by author iskandr opened on Sep 11, 2026
  1

• Add explicit cell/UMI evidence units and cell-stratified reconstruction for single-cell RNA

  openvax/isovar#226 · Filter by author iskandr opened on Sep 9, 2026
  1

• Audit all vaccine-included osteosarc variants across every RNA sample with Isovar

  openvax/isovar#218 · Filter by author iskandr opened on Sep 7, 2026
  8

• RNA sequencing coverage

  openvax/isovar#120 · Filter by author nknewnew opened on May 20, 2020

• Normalize counts by number of mapped reads to get CPM

  openvax/isovar#112 · Filter by author iskandr opened on Jun 18, 2019

• Constructing wildtype peptides

  openvax/isovar#100 · Filter by author felixfrenkel opened on Jul 12, 2018
  3

• No exon_id in mouse mm9 ensembl annotaiotn

  openvax/isovar#92 · Filter by author weizhu365 opened on Mar 9, 2018

• Isovar on multiple .bam

  openvax/isovar#91 · Filter by author JPFinnigan opened on Jan 21, 2018
  1

• Too slow running isovar. Could it be run in multithread?

  openvax/isovar#89 · Filter by author Jemimacat opened on Nov 7, 2017

• Questions about Isovar

  openvax/isovar#88 · Filter by author iskandr opened on Oct 31, 2017
  

• Figure out what to do when variant and transcript don't match

  openvax/isovar#84 · Filter by author julia326 opened on May 24, 2017

• Variant effect has a null aa_mutation_start_offset

  openvax/isovar#81 · Filter by author julia326 opened on Apr 14, 2017
  1

  

• Elongate coding sequences using reference transcripts

  enhancement
  openvax/isovar#66 · Filter by author iskandr opened on Nov 18, 2016

• Pull into Topiary

  refactor
  openvax/isovar#9 · Filter by author ihodes opened on Mar 2, 2016